Atria

Atria is designed to trim adapters and low-quality bases of next-generation sequencing data. It infers the insert DNA precisely by integrating both adapter information and reverse-complementary properties of pair-end reads within a delicate decision tree. It can also remove duplicated sequences due to PCR amplification.

If you use Atria, please cite the paper:

Jiacheng Chuan, Aiguo Zhou, Lawrence Richard Hale, Miao He, Xiang Li, Atria: an ultra-fast and accurate trimmer for adapter and quality trimming, Gigabyte, 1, 2021 https://doi.org/10.46471/gigabyte.31

Features

• FAST, even for compressed fastqs
• Highly accurate Illumina adapter trimming
• Paired-end consensus calling
• Quality trimming
• Poly X tail trimming
• Hard clip 3' and 5' ends
• N tail trimming
• Filtering reads by the number of N bases
• Filtering reads by length
• Filtering reads by read complexity
• Remove PCR duplicates (dedup)

Contents

1. Installation guide

   1.1 Release installation guide

   1.2 Install from source

2. Atria trimming methods and usages

3. Benchmark toolkit

4. Atria development notes

5. Accuracy and speed benchmark